RNA-sequencing experiments to identify differentially expressed genes between Wild Type and RBM4 KO HAP1 cell line samples

Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-Binding Motif Protein 4 (RBM4). This set of bulk RNA-sequencing experiments was performed to identify differentially expressed genes and repetitive elements, particularly HERVs, between independent Wild Type and RBM4 KO clones in the KBM-7 derived, near-haploid human cell line, HAP1 Multiple replicates are provided for each HAP1 sample: Wild Type ("WT_" ,3 replicates), RBM4 KO Clone 1 ("1B2_", 3 replicates) RBM4 KO Clone 2 ("1B6_", 2 replicates), Single-end Wild Type ("HAP1_WT_", 1 replicate) and Single-end KO Clone (HAP1_RBM4_KO_", 1 replicate)